Joe,
My graph doesn't show the increase for 2008 solely for the reason that I don't have that data. I did this paper last year and 2007 was the latest data available. It's a fair bit of work constructing this WRDS500, and I wasn't prepared to do it to add the 2008 data. Eventually, I will.
You are quite right about the tensions between debt and equity, but this tension is precisely because both constitute a claim on a corporation's earnings. Equity holders must take debt into account when assessing the value of the corporation. However, they do not see the earnings that will go to debt as not part of the expected earnings of the corporation. Quite the contrary, they merely see it as earnings that will not come to them. This measure of market capitalisation is an attempt to capture more of the claims on a corporation's earnings. Imagine what would happen to the equity value of a corporation that drastically increased its outstanding long-term debt? This is an increase in another claim on earnings, reducing the expectations for the equity holders. This will cause the equity value to decline, even though the actual expected earnings of the corporation have not changed. Retained earnings, on the other hand, could have been distributed as dividends or used to retire debt, and both would have increased the equity value of the firm. This measure is often referred to as 'enterprise value.' I retain the term 'market capitalisation' in order to keep the focus on capital and capitalisation (the same formula is at work for both debt and equity holders; also debt could serve as a proxy for the valuation of private equity firms).
For a bit on this in N&B, check out Nitzan, Differential Accumulation: Toward a New Political Economy of Capital, pp. 191-195.
If this hasn't made sense, I can try to clarify some more.
Just for the record, if you look just at equity, Wal-Mart's post 1999 decline is even more drastic.